Sequence
atgc intronic sequence ATGC exonic sequence...caatgccaatgagctttcttctagcttttgcggattcattgctgatatctactacttactaagtgattctcttgcatttgtgtgtgttctatcatgatagCTGCAATTGGCCGAGGATTGCATGAAGTACGCTATGGATTTGAGTGGTTTGTTACTACTATATTCTTCTTTGGGAGATGCTGAAGGGGTGTCAAAACTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G15980.5 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 19
caatgccaatgagctttcttctagcttttgcgga-ttcattgctgatatctact--acttactaagtgattctct-tgcatttgtgtgtgttctatcatgatagCTGCAATTGGCCGAGGATTGCATGAAGTACGCTATGGATTTGAGTGGTTTGTTACTACTATATTCTTCTTTGGGAGATGCTGAAGGGGTGTCAAAACTTG
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-agagtaagtaa---tgattctggaatgagggaacttaaatgttgattcttgttggaaatttctcttgatccattgtagctcaccatattttccattgttgcagTTAGAAATGGCTGAGGAATGTTTGAAGTATGCAATGGATTTGAGTGGCTTGTTACTGCTATATTCTTCTTTAGGAGATGCTGAAGGAATATCAAAACTTG
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 19
caatgccaatgagctttc-ttctagcttttgcgga-ttcattgctgatatctactacttac-taagtgattctcttgcatttg--tgtgtgttctatcatgatagCTGCAATTGGCCGAGGATTGCATGAAGTACGCTATGGATTTGAGTGGTTTGTTACTACTATATTCTTCTTTGGGAGATGCTGAAGGGGTGTCAAAACTTG
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-----agaataagttatgattctagaatgagggaacttaaatgttgattcttgttggaaacctctcttgacccgttgtagctcaccgtattttccattcttgcagTTAGAAATGGCTGAGGAATGTTTGAAGTATGCAATGGATTTGAGTGGCTTGTTACTGCTATATTCTTCTTTAGGAGATGCTGAAGGAATATCAAAACTTG
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 19
---caatgccaatgagctttcttctagcttttgcggattcattgctgatatctactacttactaagtgattctcttgcatttgtgtgtgttctatcatgatagCTGCAATTGGCCGAGGATTGCATGAAGTACGCTATGGATTTGAGTGGTTTGTTACTACTATATTCTTCTTTGGGAGATGCTGAAGGGGTGTCAAAACTTG
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ttcttttattcttgtcacaattaataatgattctggacacact--tgatgttgattggt-atagggtatctcttttttatctcttcattatctgttcttgcagTTAGAAATGGCCGAAGAGTGTTTAAAACAAGCAATGGATTTGAGTGGGTTATTGCTGCTATATTCTTCTTTAGGAGATGCTGAAGGAATATCAAAACTTG
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 8
caatgccaatgagctttcttctagcttttg-cggattcattgctgatatctactacttactaagtgattctcttgcatttg--tgtgtgttctatcatgatagCTGCAATTGGCCGAGGATTGCATGAAGTACGCTATGGATTTGAGTGGTTTGTTACTACTATATTCTTCTTTGGGAGATGCTGAAGGGGTGTCAAAACTTG
| | || | | | | | | | | || |||| || | || || || ||| | | | | ||| | | || | || |||| || || || | || |||| | ||||||||||| || || || |||||||||||||| |||||||||||||| | ||||||||||
---tcttgtcgcaattaataatgattctggacacacttgatgttgattggtattgggtatctctctttttcctagcaactcactttattatctgttcttgcagTTAGAAATGGCTGAAGAGTGTTTAAAACACGCAACAGATTTGAGTGGGTTATTGCTGCTATATTCTTCTTTAGGAGATGCTGAAGGAATATCAAAACTTG
upper sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 19
caatgccaatgagctttcttctagc-ttttgcggattcattgctgatat-ctactacttactaagtgattctcttgcatttgtg--tgtgttctatcatgatagCTGCAATTGGCCGAGGATTGCATGAAGTACGCTATGGATTTGAGTGGTTTGTTACTACTATATTCTTCTTTGGGAGATGCTGAAGGGGTGTCAAAACTTG
||| | | | || ||| | | || || || | | | | | | | | ||| || ||| | | |||| | | || || | || |||| ||||| || | ||| | || ||||| |||||||||||||| || || ||||||||||| ||||||||||| || | ||||||||||
----cttcgtgaattacccttcagtgctttagacaattatcacttgtaagtttttgttcattgatttaatcttttttttttttccctctgttatcttattgcagTTAGAAATGGCTGAGGAATGTTTAAAGCATGCGATGGACTTGAGTGGTTTGTTGCTGCTCTATTCTTCTTTAGGAGATGCTGACGGAATATCAAAACTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatctactacttactaagtgattctcttgcatttgtgtgtgttctatcatgatagCTGCAATTGGCCGAGGATTGCATGAAGTACGCTATGGATTTGAGTGGTTTGTTACTACTATATTCTTCTTTGGGAGATGCTGAAGGGGTGTCAAAACTTG
tacttac putative branch site (score: 1)
ttctatc putative PPT
ttactaa TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caatgccaatgagctttcttctagcttttgcggattcattgctgatatctactacttactaagtgattctcttgcatttgtgtgtgttctatcatgatagCTGCAATTGGCCGAGGATTGCATGAAGTACGCTATGGATTTGAGTGGTTTGTTACTACTATATTCTTCTTTGGGAGATGCTGAAGGGGTGTCAAAACTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG